We have a solution for this - essentially what you need to do is to 'install' the .mobileprovision file by copying it to a directory named after the UUID of the mobile provision file. This is what the Xcode Organizer actually does when you double-click a .mobileprovision file.
There's a little program called mpParse that can extract the UUID from the mobileprovision file that the script uses - link for download in the code. Then it's dead simple to copy the mobileprovision file to the correct place.
Here's a shell script I made to do this:
#!/bin/sh
# 2012 - Ben Clayton (benvium). Calvium Ltd
# Found at https://gist.github.com/2568707
#
# This script installs a .mobileprovision file without using Xcode. Unlike Xcode, it'll
# work over SSH.
#
# Requires Mac OS X (I'm using 10.7 and Xcode 4.3.2)
#
# IMPORTANT NOTE: You need to download and install the mpParse executable from http://idevblog.info/mobileprovision-files-structure-and-reading
# and place it in the same folder as this script for this to work.
#
# Usage installMobileProvisionFile.sh path/to/foobar.mobileprovision
if [ ! $# == 1 ]; then
echo "Usage: $0 (path/to/mobileprovision)"
exit
fi
mp=$1
uuid=`/usr/libexec/PlistBuddy -c 'Print UUID' /dev/stdin <<< $(security cms -D -i ${mp})`
echo "Found UUID $uuid"
output="~/Library/MobileDevice/Provisioning Profiles/$uuid.mobileprovision"
echo "copying to $output.."
cp "${mp}" "$output"
echo "done"
You can download the script direct from https://gist.github.com/2568707
Once you've run the script, you can use PROVISIONING_PROFILE and PROVISIONING_PROFILE[sdk=iphoneos*] in xcodebuild to create your app. We use this in production.
Edit: Just for reference, I asked essentially this question here a little while back ( Can an Xcode .mobileprovision file be 'installed' from the command line? ) and came up with the above when no-one seemed to know :-)
Update:
As an alternative to mpParse one could use apple tools:
/usr/libexec/PlistBuddy -c 'Print UUID' /dev/stdin <<< $(security cms -D -i path_to_mobileprovision)
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